Callable cancer loci - SEQC-II-50pc__SEQC-II_Tumor_50pc

The coverage report is generated with cacao version 0.2.1, using the following key settings:

• Genome assembly: grch38

• Mode: Hereditary cancer

• Data sources - cancer loci:

  • ClinVar - release 20181101
  • CIViC - Nov 18th 2018
  • cancerhotspots.org - version 2 (2017)

• Alignment quality threshold (MAPQ): 0

• Alignment filename: SEQC-II_Normal-ready.bam

• Target regions filename: NA

• Callability levels (germline):

  • NO_COVERAGE: No coverage (zero sequencing depth)

  • LOW_COVERAGE: Sequencing depth from 1 to 11

  • CALLABLE: Sequencing depth from 12 to 99

  • HIGH_COVERAGE: Sequencing depth above 100

Hereditary cancer - pathogenic loci

Global distribution

## ### Gene distribution

Coverage per variant locus

Callable

Gene

Locus name

ClinVar phenotype(s)

Type of locus

Low coverage

Gene

Locus name

ClinVar phenotype(s)

Type of locus

No coverage

Gene

Locus name

ClinVar phenotype(s)

Type of locus

No coverage

No loci with zero coverage found.

Predictive

No actionable loci of predictive nature with sequencing coverage.

Diagnostic

No actionable loci of diagnostic nature with sequencing coverage.

Prognostic

No actionable loci of prognostic nature with sequencing coverage.